Contacts of the helix formed by residues 19 - 33 (chain D) in PDB entry 4Q96
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 19 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D SER* 3.2 7.0 + - - -
18D ASN* 1.3 81.3 - - - +
20D GLN* 1.3 64.5 + - - +
21D HIS 3.5 1.0 + - - -
22D SER* 2.9 17.5 + - - -
23D VAL* 3.2 21.8 + - - +
208D SO4 2.5 31.0 + - - -
1618F THR* 6.3 1.1 - - - -
1619F SER* 3.7 19.5 - - - -
1620F PRO 3.6 7.0 - - - -
1621F SER* 4.1 2.5 - - - +
1622F TYR 3.7 0.7 - - - -
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Residues in contact with GLN 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLN* 3.3 28.6 - - - +
19D SER* 1.3 70.9 - - - +
21D HIS* 1.3 62.3 + - - +
23D VAL* 4.1 0.7 - - - +
24D GLN* 2.7 56.3 + - - +
65D ASP* 4.9 0.6 + - - -
204D UNX 3.6 20.2 - - - +
1620F PRO 2.8 19.1 + - - +
1621F SER 4.2 2.5 - - - +
1622F TYR* 3.2 23.6 - - - +
1623F SER 3.0 27.5 + - - -
1626F SER* 3.0 25.4 + - - -
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Residues in contact with HIS 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ARG* 3.8 40.8 + - - +
61B TYR* 6.6 0.2 - - + -
19D SER* 3.1 1.2 + - - +
20D GLN* 1.3 80.4 - - - +
22D SER* 1.3 59.3 + - - +
24D GLN* 3.7 14.8 - - - +
25D THR* 2.6 63.0 + - + +
204D UNX 4.1 2.6 + - - -
208D SO4 3.7 25.5 + - - +
1619F SER* 4.3 5.1 + - - +
1620F PRO 4.6 0.2 + - - -
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Residues in contact with SER 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLU 4.2 2.4 + - - -
16D LEU* 3.4 12.3 - - - +
17D SER* 2.9 49.6 + - - -
19D SER* 2.9 11.3 + - - -
21D HIS* 1.3 80.5 - - - +
23D VAL* 1.3 62.9 + - - +
25D THR* 3.8 3.2 - - - -
26D LEU* 3.2 24.6 + - - +
208D SO4 4.1 7.6 + - - -
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Residues in contact with VAL 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 3.9 9.4 - - + -
17D SER 3.6 16.2 - - - +
18D ASN 4.7 0.4 - - - -
19D SER 3.2 13.7 + - - +
22D SER* 1.3 77.4 - - - +
24D GLN* 1.3 56.1 + - - +
27D SER* 3.0 26.2 + - - -
58D THR* 4.0 18.2 - - + +
61D TYR* 4.0 2.0 - - + +
62D LEU* 3.6 27.7 - - - +
65D ASP* 4.1 4.7 - - + -
1622F TYR* 3.6 50.9 - - + -
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Residues in contact with GLN 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLN* 5.5 0.5 + - - -
20D GLN* 2.7 63.0 + - - +
21D HIS* 3.7 18.6 - - - +
23D VAL* 1.3 78.1 - - - +
25D THR* 1.3 61.8 + - - +
27D SER* 3.6 7.2 - - - -
28D LEU* 3.0 36.3 + - + +
65D ASP* 4.2 12.5 - - - +
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Residues in contact with THR 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D HIS* 2.6 51.5 + - + +
22D SER* 3.8 4.3 - - - -
24D GLN* 1.3 77.9 - - - +
26D LEU* 1.3 65.4 + - - +
28D LEU* 3.3 12.3 + - + +
29D TRP* 3.3 19.4 + - - +
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Residues in contact with LEU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 4.5 3.6 - - + -
12D LYS* 3.8 48.7 - - + +
13D LEU* 3.8 17.3 - - + -
16D LEU* 4.1 13.0 - - + -
22D SER 3.2 14.9 + - - +
25D THR* 1.3 76.8 - - - +
27D SER* 1.3 65.2 + - - +
29D TRP* 3.1 7.4 + - + +
30D LEU* 3.0 42.7 + - + +
62D LEU* 3.6 34.1 - - + -
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Residues in contact with SER 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D VAL 3.0 17.7 + - - -
24D GLN 3.6 3.8 - - - -
25D THR 3.3 0.2 - - - -
26D LEU* 1.3 77.6 - - - +
28D LEU* 1.3 56.5 + - - +
30D LEU* 3.4 1.7 + - - +
31D ILE* 3.0 37.4 + - - +
62D LEU* 3.6 3.3 - - - +
65D ASP* 2.7 37.4 + - - -
66D VAL* 3.4 30.6 + - - +
69D ASN* 4.4 1.0 + - - -
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Residues in contact with LEU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D GLN* 3.0 23.1 + - + +
25D THR* 3.5 13.9 - - + +
27D SER* 1.3 78.1 - - - +
29D TRP* 1.3 57.1 + - - +
31D ILE* 3.3 12.8 + - + +
32D HIS* 2.9 28.5 + - - +
69D ASN* 6.3 2.5 - - + +
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Residues in contact with TRP 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D PHE* 3.8 43.1 - + - -
8D ALA* 4.2 15.9 - - + -
9D LEU* 4.6 9.6 - - - -
12D LYS* 3.7 44.5 - - + +
25D THR* 3.3 9.0 + - + +
26D LEU* 3.1 14.1 + - + +
28D LEU* 1.3 79.0 - - - +
30D LEU* 1.3 81.3 + - + +
32D HIS* 3.0 14.7 + + + +
33D HIS* 2.9 59.9 + + - -
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D PHE* 5.1 0.2 - - + -
9D LEU* 3.6 27.1 - - + -
26D LEU* 3.0 21.5 + - + +
27D SER 3.7 3.6 - - - +
29D TRP* 1.3 90.0 - - + +
31D ILE* 1.3 63.2 + - - +
33D HIS* 3.1 6.1 + - - +
34D ARG 3.1 17.5 + - - -
40D ILE* 4.1 31.4 - - + -
44D TRP* 6.1 1.1 - - + -
62D LEU* 4.0 23.8 - - + -
66D VAL* 3.9 25.1 - - + -
77D PHE* 3.4 19.9 - - + -
81D PHE* 6.4 0.7 - - + -
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Residues in contact with ILE 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D SER* 3.0 29.8 + - - +
28D LEU* 3.8 12.6 - - + +
30D LEU* 1.3 72.4 - - - +
32D HIS* 1.3 65.8 + - - +
34D ARG* 3.2 29.8 + - - +
66D VAL* 4.0 17.0 - - + +
69D ASN* 3.4 35.7 - - + +
70D SER* 3.6 18.8 - - - +
73D LYS* 4.1 26.9 - - + -
77D PHE* 4.2 5.8 - - + -
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Residues in contact with HIS 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D LEU 2.9 14.3 + - - +
29D TRP* 3.1 17.9 - + + +
31D ILE* 1.3 79.5 - - - +
33D HIS* 1.3 83.4 + + - +
34D ARG* 3.3 11.6 + - - +
35D LYS* 5.1 1.7 + - - +
209D SO4 5.1 0.9 + - - -
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Residues in contact with HIS 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D PHE* 3.5 21.1 + - + +
29D TRP* 2.9 71.1 + + - +
30D LEU* 3.1 7.8 + - - +
32D HIS* 1.3 98.0 + + - +
34D ARG* 1.3 56.4 + - - +
35D LYS* 3.1 5.2 - - - +
36D HIS* 3.0 29.2 + - + -
40D ILE* 3.3 14.1 - - + +
209D SO4 2.8 39.2 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il